Average non-synonymous site divergence/synonymous site divergence ( d
) values for genes classified into developmental stages based on expressed sequence tag (EST) data. Averages are shown with permuted 95% confidence intervals (95% CIs) for each specificity threshold (from left to right, in increasing contrast): no specificity threshold, greater than twofold, fourfold, or eightfold proportion of representation relative to other stages, and unique to a single developmental stage. Larval/pupal represents the pooled larval and pupal stages. The differences in the distributions between stages within a specificity threshold were found to be statistically significant for most thresholds (P < 0.01). Furthermore the differences between thresholds within a stage were also found to be statistically significant in most pairwise comparisons (P < 0.05) (Additional file 7).